A federal judge denied a Texas school district’s request to throw out a lawsuit that alleges the district violated an agnostic student’s first amendment rights by allowing prayers at school functions.

The move on Wednesday is the latest development in the prayer controversy that dates back almost a year and has flip-flopped through the courts, causing public outrage on both sides of the issue.

The family of agnostic student Corwyn Schultz filed a lawsuit in May against the school district. Chief United States District Judge Fred Biery banned organized prayer at the Medina Valley High School graduation in June.

An appellate court, however, overturned the decision, and prayer was allowed at the graduation in Castroville, Texas. Schultz and his family did not attend the graduation ceremony because of fear of retribution for suing, according to reports.

Biery ruled against the school district again Wednesday and allowed current students to join the lawsuit anonymously, the San Antonio Express News reported.

Schultz alleges in the suit that his previous complaints were ignored and he was retaliated against for complaining to school officials.

Biery’s court ruling suggested Schultz and the district should enter into mediation to end the costly lawsuit.

“The parties are spending what appears to be inordinate amounts of money and time which could be better spent on educating students,” wrote the judge.

However, both sides seem entrenched in their beliefs, leaving a lengthy court battle likely.

“The district wholeheartedly stands behind the fundamental and important principles of the Constitution and believes that student freedom of expression is a right that cannot be taken away or negotiated through mediation,” said the district in a statement.

Litigation is slated to begin at the end of the year, according to reports.

Similar court cases may pop up in Florida if the state eventually votes to allow school prayer.

A bill allowing prayers at some school events passed a vote by Florida’s Senate Education Committee Wednesday by a 4 to 1 margin.

Opposition groups, such as the Anti-Defamation League and American Civil Liberties Union, quickly floated the idea of a lawsuit if the bill moved closer to becoming law.

"State-sponsored school prayer is unfair and inappropriate because our public schools are for people of all faiths," said Anti-Defamation League lobbyist David Barkey to the Sun Times.